TITLE File : 53a6_beta.mtb Force field : 53A6 (condensed-phase simulations) Reference : Oostenbrink et al. J. Comput. Chem. 2004, 25, 1656-1676 File content : molecular topology building blocks (beta amino acids) Format : GROMOS11 Initial file : PHH, Zuerich, May 2011 Time stamp : PHH, Thu Nov 10 22:13:50 CET 2011 Remark : ***warning*** this file is an auxiliary mtb file - since Nov 2011, these files no longer contain blocks that were redundant with those of the corresponding main mtb file. As a result, make_top must always be called with inclusion of the main mtb file in addition to possible auxiliary ones. Remark : Change from 53A(B)5 involves different charges for the polar amino-acid sidechains Remark : Parameterization against hydration properties of model compounds Remark : This file only differs from the corresponding file in 53A(B)5 in the charges of polar amino-acid sidechains Remark : DG, NS, Oct 07: exclusion errors corrected in FMNR, ATP, TMP, THF and HEME Remark : DG, CO, Jan 08: errors in improper dihedrals 21-24 in NADH corrected Remark : The above changes are propagated to subsequent force-field versions Remark : PHH, May 2011 - finalized GROMOS11 file distribution - enforced sequential ordering by (central) atom numbers in covalent terms for all files (no effect on GROMOS11 make_top; make_top enforced it anyway, but now, we avoid the big list of warnings) Modifications : [list below changes after May 2011 - with initials, location and date - and update time stamp] PHH, 09.11.2011: Reintroduced a FORCEFIELD block in all GROMOS11 files. PHH, 09.11.2011: Removed all MTBUILDBLSOLVENT blocks from all auxiliary mtb files (now only included in the main mtb file). As a result, make_top must now always be called with inclusion of the main mtb file (in addition to the possible auxiliary ones). PHH, 09.11.2011: Introduced specific patches for the beta-peptides BH3+, BH2, BOOH and BOO- are like NH3+ (with CA renamed to CB) NH2 (with CA renamed to CB), COOH and COO- of the alpha-peptides (the patch NPRO of the alpha-peptides was not ported). END FORCEFIELD 53A6 END # Building blocks to be (re)introduced: heme PHYSICALCONSTANTS # FPEPSI: 1.0/(4.0*PI*EPS0) (EPS0 is the permittivity of vacuum) 0.1389354E+03 # HBAR: Planck's constant HBAR = H/(2* PI) 0.6350780E-01 # SPDL: Speed of light (in nm/ps) 2.9979245800E05 # BOLTZ: Boltzmann's constant 8.31441E-03 END LINKEXCLUSIONS #nearest neighbour exclusions when linking #NRNE 2 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE RAF # building block (residue, nucleotide, etc.) # RNME RAF # number of atoms, number of preceding exclusions # NMAT NLIN 18 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 3 2 3 4 2 H 21 1 0.31000 1 1 3 3 CB 15 4 0.00000 1 3 4 5 17 4 CA 14 3 0.00000 0 5 5 6 17 18 19 5 CG 15 4 0.00000 0 8 6 7 8 9 10 11 13 17 6 CD 12 12 0.00000 1 9 7 8 9 10 11 12 13 14 15 7 CE1 12 12 -0.14000 0 8 8 9 10 11 12 13 15 16 8 HE1 20 1 0.14000 1 4 9 11 12 15 9 CE2 12 12 -0.14000 0 6 10 11 13 14 15 16 10 HE2 20 1 0.14000 1 3 13 14 15 11 CZ1 12 12 -0.14000 0 5 12 13 14 15 16 12 HZ1 20 1 0.14000 1 3 13 15 16 13 CZ2 12 12 -0.14000 0 3 14 15 16 14 HZ2 20 1 0.14000 1 2 15 16 15 CH 12 12 -0.14000 0 1 16 16 HH 20 1 0.14000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 17 C 12 12 0.45000 0 18 O 1 16 -0.45000 1 # bonds # NB 19 # IB JB MCB 1 2 2 1 3 21 4 5 27 3 4 27 5 6 27 6 7 16 6 9 16 7 8 3 7 11 16 9 10 3 9 13 16 11 12 3 11 15 16 13 14 3 13 15 16 15 16 3 4 17 27 17 18 5 17 19 10 # bond angles # NBA 29 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 3 4 5 13 1 3 4 13 5 4 17 13 4 5 6 15 5 6 7 27 5 6 9 27 7 6 9 27 6 7 8 25 6 7 11 27 8 7 11 25 6 9 10 25 6 9 13 27 10 9 13 25 7 11 12 25 7 11 15 27 12 11 15 25 9 13 14 25 9 13 15 27 14 13 15 25 11 15 13 27 11 15 16 25 13 15 16 25 3 4 17 15 4 17 18 30 4 17 19 19 18 17 19 33 # improper dihedrals # NIDA 15 # IB JB KB LB MCB 1 -1 3 2 1 # 4 17 3 5 2 this is for SAF # 4 17 5 3 2 4 3 17 5 2 6 7 9 5 1 6 7 11 15 1 6 9 13 15 1 7 6 9 13 1 7 6 11 8 1 7 11 15 13 1 9 6 7 11 1 9 6 13 10 1 9 13 15 11 1 12 7 15 11 1 14 9 15 13 1 15 11 13 16 1 17 4 19 18 1 # dihedrals # NDA 6 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 4 39 3 4 5 6 34 1 3 4 17 34 4 5 6 7 40 3 4 17 19 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE RAV # building block (residue, nucleotide, etc.) # RNME RAV # number of atoms, number of preceding exclusions # NMAT NLIN 9 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 3 2 3 4 2 H 21 1 0.31000 1 1 3 3 CB 15 4 0.00000 1 3 4 5 8 4 CA 14 3 0.00000 0 6 5 6 7 8 9 10 5 CG 14 3 0.00000 0 3 6 7 8 6 CD1 16 5 0.00000 0 1 7 7 CD2 16 5 0.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 8 C 12 12 0.45000 0 9 O 1 16 -0.45000 1 # bonds # NB 9 # IB JB MCB 1 2 2 1 3 21 3 4 27 4 5 27 4 8 27 5 6 27 5 7 27 8 9 5 8 10 10 # bond angles # NBA 13 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 3 4 5 15 3 4 8 15 5 4 8 15 4 5 6 15 4 5 7 15 6 5 7 15 4 8 9 30 4 8 10 19 9 8 10 33 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 4 6 7 5 2 4 3 8 5 2 8 4 10 9 1 # dihedrals # NDA 5 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 4 39 1 3 4 8 34 3 4 5 6 34 3 4 8 10 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE RBCH # building block (residue, nucleotide, etc.) # RNME RBCH # stereochemistry at CB atom -> R # improper dihedral angle definition -> CB-N-CA-CG = 35 deg # number of atoms, number of preceding exclusions # NMAT NLIN 9 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 7 2 H 21 1 0.31000 1 1 3 3 CB 14 3 0.00000 1 4 4 5 7 8 4 CG 15 4 0.15000 0 3 5 6 7 5 SD 23 32 -0.37000 0 1 6 6 HD 21 1 0.22000 1 0 7 CA 15 4 0.00000 1 3 8 9 10 # trailing atoms #ATOM ANM IACM MASS CGMICGM 8 C 12 12 0.45000 0 9 O 1 16 -0.45000 1 # bonds # NB 9 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 7 27 4 5 32 5 6 8 7 8 27 8 9 5 8 10 10 # bond angles # NBA 12 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 7 13 4 3 7 13 3 4 5 16 4 5 6 3 3 7 8 15 7 8 9 30 7 8 10 19 9 8 10 33 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 3 1 7 4 2 8 7 10 9 1 # dihedrals # NDA 6 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 7 39 1 3 4 5 34 1 3 7 8 34 3 4 5 6 26 3 7 8 10 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE RBI # building block (residue, nucleotide, etc.) # RNME RBI # stereochemistry at CB atom -> R # improper dihedral angle definition -> CB-N-CA-CG = 35 deg # number of atoms, number of preceding exclusions # NMAT NLIN 10 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 8 2 H 21 1 0.31000 1 1 3 3 CB 14 3 0.00000 1 5 4 5 6 8 9 4 CG 14 3 0.00000 0 4 5 6 7 8 5 CD1 15 4 0.00000 0 2 6 7 6 CD2 16 5 0.00000 0 0 7 CE 16 5 0.00000 1 0 8 CA 15 4 0.00000 1 3 9 10 11 # trailing atoms #ATOM ANM IACM MASS CGMICGM 9 C 12 12 0.45000 0 10 O 1 16 -0.45000 1 # bonds # NB 10 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 8 27 4 5 27 4 6 27 5 7 27 8 9 27 9 10 5 9 11 10 # bond angles # NBA 14 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 8 13 4 3 8 13 3 4 5 15 3 4 6 15 5 4 6 15 4 5 7 15 3 8 9 15 8 9 10 30 8 9 11 19 10 9 11 33 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 3 1 8 4 2 4 5 6 3 2 9 8 11 10 1 # dihedrals # NDA 6 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 8 39 1 3 4 5 34 1 3 8 9 34 3 4 5 7 34 3 8 9 11 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE RBKH # building block (residue, nucleotide, etc.) # RNME RBKH # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 12 2 H 21 1 0.31000 1 1 3 3 CB 14 3 0.00000 0 4 4 5 12 13 4 CG 15 4 0.00000 1 3 5 6 12 5 CD 15 4 0.00000 0 2 6 7 6 CE 15 4 0.00000 1 2 7 8 7 CZ 15 4 0.12700 0 4 8 9 10 11 8 NH 8 14 0.12900 0 3 9 10 11 9 HH1 21 1 0.24800 0 2 10 11 10 HH2 21 1 0.24800 0 1 11 11 HH3 21 1 0.24800 1 0 12 CA 15 4 0.00000 1 3 13 14 15 # trailing atoms #ATOM ANM IACM MASS CGMICGM 13 C 12 12 0.45000 0 14 O 1 16 -0.45000 1 # bonds # NB 14 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 12 27 4 5 27 5 6 27 6 7 27 7 8 21 8 9 2 8 10 2 8 11 2 12 13 27 13 14 5 13 15 10 # bond angles # NBA 20 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 12 13 4 3 12 15 3 4 5 15 4 5 6 15 5 6 7 15 6 7 8 15 7 8 9 11 7 8 10 11 7 8 11 11 9 8 10 10 9 8 11 10 10 8 11 10 3 12 13 15 12 13 14 30 12 13 15 19 14 13 15 33 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 # 3 1 12 4 2 # 3 1 4 12 2 4 1 12 3 2 13 12 15 14 1 # dihedrals # NDA 9 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 12 39 1 3 4 5 34 1 3 12 13 34 3 4 5 6 34 4 5 6 7 34 5 6 7 8 34 6 7 8 9 29 3 12 13 15 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE RBM # building block (residue, nucleotide, etc.) # RNME RBM # stereochemistry at CB atom -> R # improper dihedral angle definition -> CB-N-CA-CG = 35 deg # number of atoms, number of preceding exclusions # NMAT NLIN 10 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 8 2 H 21 1 0.31000 1 1 3 3 CB 14 3 0.00000 0 4 4 5 8 9 4 CG 15 4 0.00000 1 3 5 6 8 5 CD 15 4 0.24100 0 2 6 7 6 SE 23 32 -0.48200 0 1 7 7 CZ 16 5 0.24100 1 0 8 CA 15 4 0.00000 1 3 9 10 11 # trailing atoms #ATOM ANM IACM MASS CGMICGM 9 C 12 12 0.45000 0 10 O 1 16 -0.45000 1 # bonds # NB 10 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 8 27 4 5 27 5 6 32 6 7 31 8 9 27 9 10 5 9 11 10 # bond angles # NBA 13 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 8 13 4 3 8 13 3 4 5 15 4 5 6 16 5 6 7 4 3 8 9 15 8 9 10 30 8 9 11 19 10 9 11 33 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 3 1 8 4 2 9 8 11 10 1 # dihedrals # NDA 7 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 8 39 1 3 4 5 34 1 3 8 9 34 3 4 5 6 34 4 5 6 7 26 3 8 9 11 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE RBN # building block (residue, nucleotide, etc.) # RNME RBN # stereochemistry at CB atom -> S # improper dihedral angle definition -> CB-CA-N-CG = 35 deg # number of atoms, number of preceding exclusions # NMAT NLIN 12 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 10 2 H 21 1 0.31000 1 1 3 3 CB 14 3 0.00000 0 4 4 5 10 11 4 CG 15 4 0.00000 1 4 5 6 7 10 5 CD 12 12 0.29000 0 4 6 7 8 9 6 OE1 1 16 -0.45000 0 1 7 7 NE2 7 14 -0.72000 0 2 8 9 8 HE21 21 1 0.44000 0 1 9 9 HE22 21 1 0.44000 1 0 10 CA 15 4 0.00000 1 3 11 12 13 # trailing atoms #ATOM ANM IACM MASS CGMICGM 11 C 12 12 0.45000 0 12 O 1 16 -0.45000 1 # bonds # NB 12 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 10 27 4 5 27 5 6 5 5 7 9 7 8 2 7 9 2 10 11 27 11 12 5 11 13 10 # bond angles # NBA 17 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 10 13 4 3 10 13 3 4 5 15 4 5 6 30 4 5 7 19 6 5 7 33 5 7 8 23 5 7 9 23 8 7 9 24 3 10 11 15 10 11 12 30 10 11 13 19 12 11 13 33 # improper dihedrals # NIDA 5 # IB JB KB LB MCB 1 -1 3 2 1 4 1 10 3 2 5 6 7 4 1 7 8 9 5 1 11 10 13 12 1 # dihedrals # NDA 7 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 10 39 1 3 4 5 34 1 3 10 11 34 3 4 5 7 40 4 5 7 8 14 3 10 11 13 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE RBS # building block (residue, nucleotide, etc.) # RNME RBS # stereochemistry at CB atom -> R # improper dihedral angle definition -> CB-N-CA-CG = 35 deg # number of atoms, number of preceding exclusions # NMAT NLIN 9 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 7 2 H 21 1 0.31000 1 1 3 3 CB 14 3 0.00000 1 4 4 5 7 8 4 CG 15 4 0.26600 0 3 5 6 7 5 OD 3 16 -0.67400 0 1 6 6 HD 21 1 0.40800 1 0 7 CA 15 4 0.00000 1 3 8 9 10 # trailing atoms #ATOM ANM IACM MASS CGMICGM 8 C 12 12 0.45000 0 9 O 1 16 -0.45000 1 # bonds # NB 9 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 7 27 4 5 18 5 6 1 7 8 27 8 9 5 8 10 10 # bond angles # NBA 12 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 7 13 4 3 7 13 3 4 5 13 4 5 6 12 3 7 8 15 7 8 9 30 7 8 10 19 9 8 10 33 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 3 1 7 4 2 8 7 10 9 1 # dihedrals # NDA 6 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 7 39 1 3 4 5 34 1 3 7 8 34 3 4 5 6 23 3 7 8 10 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE RBSP # building block (residue, nucleotide, etc.) # RNME RBSP # R-CB-propane substituted Serine (RBSP) # stereochemistry at CB atom -> R # improper dihedral angle definition -> CB-N-CA-CG = 35 deg # number of atoms, number of preceding exclusions # NMAT NLIN 11 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 9 2 H 21 1 0.31000 1 1 3 3 CB 14 3 0.00000 1 4 4 5 9 10 4 CG 15 4 0.16200 0 3 5 6 9 5 OD 4 16 -0.32400 0 2 6 7 6 CE 15 4 0.16200 1 2 7 8 7 CZ 14 3 0.00000 0 1 8 8 CH 15 4 0.00000 1 0 9 CA 15 4 0.00000 1 3 10 11 12 # trailing atoms #ATOM ANM IACM MASS CGMICGM 10 C 12 12 0.45000 0 11 O 1 16 -0.45000 1 # bonds # NB 11 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 9 27 4 5 18 5 6 18 6 7 27 7 8 10 9 10 27 10 11 5 10 12 10 # bond angles # NBA 14 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 9 13 4 3 9 15 3 4 5 15 4 5 6 12 5 6 7 15 6 7 8 30 # 10 3 9 10 15 9 10 11 30 9 10 12 19 11 10 12 33 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 3 1 9 4 2 10 9 12 11 1 # dihedrals # NDA 8 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 9 39 1 3 4 5 34 1 3 9 10 34 3 9 10 12 40 3 4 5 6 23 4 5 6 7 23 5 6 7 8 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE RBT # building block (residue, nucleotide, etc.) # RNME RBT # stereochemistry at CB atom -> R # improper dihedral angle definition -> CB-N-CA-CG = 35 deg # number of atoms, number of preceding exclusions # NMAT NLIN 10 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 8 2 H 21 1 0.31000 1 1 3 3 CB 14 3 0.00000 1 5 4 5 7 8 9 4 CG 14 3 0.26600 0 4 5 6 7 8 5 OD1 3 16 -0.67400 0 2 6 7 6 HD1 21 1 0.40800 1 0 7 CD2 16 5 0.00000 1 0 8 CA 15 4 0.00000 1 3 9 10 11 # trailing atoms #ATOM ANM IACM MASS CGMICGM 9 C 12 12 0.45000 0 10 O 1 16 -0.45000 1 # bonds # NB 10 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 8 27 4 5 18 4 7 27 5 6 1 8 9 27 9 10 5 9 11 10 # bond angles # NBA 14 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 8 13 4 3 8 13 3 4 5 13 3 4 7 15 5 4 7 15 4 5 6 12 3 8 9 15 8 9 10 30 8 9 11 19 10 9 11 33 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 3 1 8 4 2 4 5 7 3 2 9 8 11 10 1 # dihedrals # NDA 6 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 8 39 1 3 4 5 34 1 3 8 9 34 3 4 5 6 23 3 8 9 11 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE RBV # building block (residue, nucleotide, etc.) # RNME RBV # stereochemistry at CB atom -> R # improper dihedral angle definition -> CB-N-CA-CG = 35 deg # number of atoms, number of preceding exclusions # NMAT NLIN 9 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 7 2 H 21 1 0.31000 1 1 3 3 CB 14 3 0.00000 0 5 4 5 6 7 8 4 CG 14 3 0.00000 0 3 5 6 7 5 CD1 16 5 0.00000 0 1 6 6 CD2 16 5 0.00000 1 0 7 CA 15 4 0.00000 1 3 8 9 10 # trailing atoms #ATOM ANM IACM MASS CGMICGM 8 C 12 12 0.45000 0 9 O 1 16 -0.45000 1 # bonds # NB 9 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 7 27 4 5 27 4 6 27 7 8 27 8 9 5 8 10 10 # bond angles # NBA 13 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 7 13 4 3 7 15 3 4 5 15 3 4 6 15 5 4 6 15 3 7 8 15 7 8 9 30 7 8 10 19 9 8 10 33 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 3 1 7 4 2 3 5 6 4 2 8 7 10 9 1 # dihedrals # NDA 5 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 7 39 1 3 4 5 34 1 3 7 8 34 3 7 8 10 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE SAA # building block (residue, nucleotide, etc.) # RNME SAA # stereochemistry at CA atom -> S # improper dihedral angle definition -> CA-C-CB-CG = 35 deg # number of atoms, number of preceding exclusions # NMAT NLIN 7 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 3 2 3 4 2 H 21 1 0.31000 1 1 3 3 CB 15 4 0.00000 1 3 4 5 6 4 CA 14 3 0.00000 0 4 5 6 7 8 5 CG 16 5 0.00000 1 1 6 # trailing atoms #ATOM ANM IACM MASS CGMICGM 6 C 12 12 0.45000 0 7 O 1 16 -0.45000 1 # bonds # NB 7 # IB JB MCB 1 2 2 1 3 21 3 4 27 4 5 27 4 6 27 6 7 5 6 8 10 # bond angles # NBA 10 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 3 4 5 15 3 4 6 15 5 4 6 15 4 6 7 30 4 6 8 19 7 6 8 33 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 5 3 6 4 2 6 4 8 7 1 # dihedrals # NDA 4 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 4 39 1 3 4 6 34 3 4 6 8 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE SAF # building block (residue, nucleotide, etc.) # RNME SAF # number of atoms, number of preceding exclusions # NMAT NLIN 18 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 3 2 3 4 2 H 21 1 0.31000 1 1 3 3 CB 15 4 0.00000 1 3 4 5 17 4 CA 14 3 0.00000 0 5 5 6 17 18 19 5 CG 15 4 0.00000 0 8 6 7 8 9 10 11 13 17 6 CD 12 12 0.00000 1 9 7 8 9 10 11 12 13 14 15 7 CE1 12 12 -0.14000 0 8 8 9 10 11 12 13 15 16 8 HE1 20 1 0.14000 1 4 9 11 12 15 9 CE2 12 12 -0.14000 0 6 10 11 13 14 15 16 10 HE2 20 1 0.14000 1 3 13 14 15 11 CZ1 12 12 -0.14000 0 5 12 13 14 15 16 12 HZ1 20 1 0.14000 1 3 13 15 16 13 CZ2 12 12 -0.14000 0 3 14 15 16 14 HZ2 20 1 0.14000 1 2 15 16 15 CH 12 12 -0.14000 0 1 16 16 HH 20 1 0.14000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 17 C 12 12 0.45000 0 18 O 1 16 -0.45000 1 # bonds # NB 19 # IB JB MCB 1 2 2 1 3 21 4 5 27 3 4 27 5 6 27 6 7 16 6 9 16 7 8 3 7 11 16 9 10 3 9 13 16 11 12 3 11 15 16 13 14 3 13 15 16 15 16 3 4 17 27 17 18 5 17 19 10 # bond angles # NBA 29 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 3 4 5 13 1 3 4 13 5 4 17 13 4 5 6 15 5 6 7 27 5 6 9 27 7 6 9 27 6 7 8 25 6 7 11 27 8 7 11 25 6 9 10 25 6 9 13 27 10 9 13 25 7 11 12 25 7 11 15 27 12 11 15 25 9 13 14 25 9 13 15 27 14 13 15 25 11 15 13 27 11 15 16 25 13 15 16 25 3 4 17 15 4 17 18 30 4 17 19 19 18 17 19 33 # improper dihedrals # NIDA 15 # IB JB KB LB MCB 1 -1 3 2 1 5 3 17 4 2 6 7 9 5 1 6 7 11 15 1 6 9 13 15 1 7 6 9 13 1 7 6 11 8 1 7 11 15 13 1 9 6 7 11 1 9 6 13 10 1 9 13 15 11 1 12 7 15 11 1 14 9 15 13 1 15 11 13 16 1 17 4 19 18 1 # dihedrals # NDA 6 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 4 39 3 4 5 6 34 1 3 4 17 34 4 5 6 7 40 3 4 17 19 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE SAFF # building block (residue, nucleotide, etc.) # RNME SAFF # # alpha-F RAF : similar to RAF # # number of atoms, number of preceding exclusions # NMAT NLIN 19 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 3 2 3 4 2 H 21 1 0.31000 1 1 3 3 CB 14 3 0.00000 1 4 4 5 6 18 4 CA 15 4 0.20000 0 6 5 6 7 18 19 20 # ============================= 5 F 32 19 -0.20000 0 4 6 18 19 20 # ============================= 6 CG 15 4 0.00000 0 8 7 8 9 10 11 12 14 18 7 CD 12 12 0.00000 1 9 8 9 10 11 12 13 14 15 16 8 CE1 12 12 -0.14000 0 8 9 10 11 12 13 14 16 17 9 HE1 20 1 0.14000 1 4 10 12 13 16 10 CE2 12 12 -0.14000 0 6 11 12 14 15 16 17 11 HE2 20 1 0.14000 1 3 14 15 16 12 CZ1 12 12 -0.14000 0 5 13 14 15 16 17 13 HZ1 20 1 0.14000 1 3 14 16 17 14 CZ2 12 12 -0.14000 0 3 15 16 17 15 HZ2 20 1 0.14000 1 2 16 17 16 CH 12 12 -0.14000 0 1 17 17 HH 20 1 0.14000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 18 C 12 12 0.45000 0 19 O 1 16 -0.45000 1 # bonds # NB 20 # IB JB MCB 1 2 2 1 3 21 4 6 27 3 4 27 6 7 27 7 8 16 7 10 16 8 9 3 8 12 16 10 11 3 10 14 16 12 13 3 12 16 16 14 15 3 14 16 16 16 17 3 18 19 5 18 20 10 4 18 27 # new addition for C-F bond 4 5 13 # bond angles # NBA 32 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 3 4 6 13 1 3 4 13 6 4 18 13 4 6 7 15 6 7 8 27 6 7 10 27 8 7 10 27 7 8 9 25 7 8 12 27 9 8 12 25 7 10 11 25 7 10 14 27 11 10 14 25 8 12 13 25 8 12 16 27 13 12 16 25 10 14 15 25 10 14 16 27 15 14 16 25 12 16 14 27 12 16 17 25 14 16 17 25 3 4 18 15 4 18 19 30 4 18 20 19 19 18 20 33 3 4 5 15 5 4 6 15 5 4 18 15 # improper dihedrals # NIDA 15 # IB JB KB LB MCB 1 -1 3 2 1 # 4 18 3 6 2 # 4 18 6 3 2 4 3 18 6 2 7 8 10 6 1 7 8 12 16 1 7 10 14 16 1 8 7 10 14 1 8 7 12 9 1 8 12 16 14 1 10 7 8 12 1 10 7 14 11 1 10 14 16 12 1 13 8 16 12 1 15 10 16 14 1 16 12 14 17 1 18 4 20 19 1 # dihedrals # NDA 6 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 4 39 3 4 6 7 34 1 3 4 18 34 4 6 7 8 40 3 4 18 20 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE SAL # building block (residue, nucleotide, etc.) # RNME SAL # stereochemistry at CA atom -> S # improper dihedral angle definition -> CA-C-CB-CG = 35 deg # number of atoms, number of preceding exclusions # NMAT NLIN 10 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 3 2 3 4 2 H 21 1 0.31000 1 1 3 3 CB 15 4 0.00000 1 3 4 5 9 4 CA 14 3 0.00000 0 5 5 6 9 10 11 5 CG 15 4 0.00000 1 4 6 7 8 9 6 CD 14 3 0.00000 0 2 7 8 7 CE1 16 5 0.00000 0 1 8 8 CE2 16 5 0.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 9 C 12 12 0.45000 0 10 O 1 16 -0.45000 1 # bonds # NB 10 # IB JB MCB 1 2 2 1 3 21 3 4 27 4 5 27 4 9 27 5 6 27 6 7 27 6 8 27 9 10 5 9 11 10 # bond angles # NBA 14 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 3 4 5 15 3 4 9 15 5 4 9 15 4 5 6 15 5 6 7 15 5 6 8 15 7 6 8 15 4 9 10 30 4 9 11 19 10 9 11 33 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 5 3 9 4 2 5 7 8 6 2 9 4 11 10 1 # dihedrals # NDA 6 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 4 39 1 3 4 9 34 3 4 5 6 34 3 4 9 11 40 4 5 6 7 34 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE SAM # building block (residue, nucleotide, etc.) # RNME SAM # stereochemistry at CA atom -> S # improper dihedral angle definition -> CA-C-CB-CG = 35 deg # number of atoms, number of preceding exclusions # NMAT NLIN 10 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 3 2 3 4 2 H 21 1 0.31000 1 1 3 3 CB 15 4 0.00000 1 3 4 5 9 4 CA 14 3 0.00000 0 5 5 6 9 10 11 5 CG 15 4 0.00000 1 3 6 7 9 6 CD 15 4 0.24100 0 2 7 8 7 SE 23 32 -0.48200 0 1 8 8 CZ 16 5 0.24100 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 9 C 12 12 0.45000 0 10 O 1 16 -0.45000 1 # bonds # NB 10 # IB JB MCB 1 2 2 1 3 21 3 4 27 4 9 27 4 5 27 5 6 27 6 7 32 #8 9 31 7 8 31 9 10 5 9 11 10 # bond angles # NBA 13 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 3 4 9 15 5 4 9 15 3 4 5 15 4 5 6 15 5 6 7 16 6 7 8 4 4 9 10 30 4 9 11 19 10 9 11 33 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 5 3 9 4 2 9 4 11 10 1 # dihedrals # NDA 7 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 4 39 1 3 4 9 34 3 4 5 6 34 4 5 6 7 34 5 6 7 8 26 3 4 9 11 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE SAV # building block (residue, nucleotide, etc.) # RNME SAV # stereochemistry at CA atom -> S # improper dihedral angle definition -> CA-C-CB-CG = 35 deg # number of atoms, number of preceding exclusions # NMAT NLIN 9 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 3 2 3 4 2 H 21 1 0.31000 1 1 3 3 CB 15 4 0.00000 1 3 4 5 8 4 CA 14 3 0.00000 0 6 5 6 7 8 9 10 5 CG 14 3 0.00000 0 3 6 7 8 6 CD1 16 5 0.00000 0 1 7 7 CD2 16 5 0.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 8 C 12 12 0.45000 0 9 O 1 16 -0.45000 1 # bonds # NB 9 # IB JB MCB 1 2 2 1 3 21 3 4 27 4 5 27 4 8 27 5 6 27 5 7 27 8 9 5 8 10 10 # bond angles # NBA 13 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 3 4 5 15 3 4 8 15 5 4 8 15 4 5 6 15 4 5 7 15 6 5 7 15 4 8 9 30 4 8 10 19 9 8 10 33 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 4 6 7 5 2 5 3 8 4 2 8 4 10 9 1 # dihedrals # NDA 5 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 4 39 1 3 4 8 34 3 4 5 6 34 3 4 8 10 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE SBA # building block (residue, nucleotide, etc.) # RNME SBA # stereochemistry at CB atom -> S # improper dihedral angle definition -> CB-N-CA-CG = 35 deg # number of atoms, number of preceding exclusions # NMAT NLIN 7 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 5 2 H 21 1 0.31000 1 1 3 3 CB 14 3 0.00000 0 3 4 5 6 4 CG 16 5 0.00000 1 1 5 5 CA 15 4 0.00000 1 3 6 7 8 # trailing atoms #ATOM ANM IACM MASS CGMICGM 6 C 12 12 0.45000 0 7 O 1 16 -0.45000 1 # bonds # NB 7 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 5 27 5 6 27 6 7 5 6 8 10 # bond angles # NBA 10 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 5 13 4 3 5 15 3 5 6 15 5 6 7 30 5 6 8 19 7 6 8 33 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 3 1 5 4 2 6 5 8 7 1 # dihedrals # NDA 4 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 5 39 1 3 5 6 34 3 5 6 8 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE SBCH # building block (residue, nucleotide, etc.) # RNME SBCH # stereochemistry at CB atom -> S # improper dihedral angle definition -> CB-CA-N-CG = 35 deg # number of atoms, number of preceding exclusions # NMAT NLIN 9 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 7 2 H 21 1 0.31000 1 1 3 3 CB 14 3 0.00000 1 4 4 5 7 8 4 CG 15 4 0.15000 0 3 5 6 7 5 SD 23 32 -0.37000 0 1 6 6 HD 21 1 0.22000 1 0 7 CA 15 4 0.00000 1 3 8 9 10 # trailing atoms #ATOM ANM IACM MASS CGMICGM 8 C 12 12 0.45000 0 9 O 1 16 -0.45000 1 # bonds # NB 9 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 7 27 4 5 32 5 6 8 7 8 27 8 9 5 8 10 10 # bond angles # NBA 12 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 7 13 4 3 7 13 3 4 5 16 4 5 6 3 3 7 8 15 7 8 9 30 7 8 10 19 9 8 10 33 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 4 1 7 3 2 8 7 10 9 1 # dihedrals # NDA 6 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 7 39 1 3 4 5 34 1 3 7 8 34 3 4 5 6 26 3 7 8 10 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE SBD # building block (residue, nucleotide, etc.) # RNME SBD # stereochemistry at CB atom -> S # improper dihedral angle definition -> CB-CA-N-CG = 35 deg # number of atoms, number of preceding exclusions # NMAT NLIN 10 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 8 2 H 21 1 0.31000 1 1 3 3 CB 14 3 0.00000 0 4 4 5 8 9 4 CG 15 4 0.00000 1 4 5 6 7 8 5 CD 12 12 0.27000 0 2 6 7 6 OE1 2 16 -0.63500 0 1 7 7 OE2 2 16 -0.63500 1 0 8 CA 15 4 0.00000 1 3 9 10 11 # trailing atoms #ATOM ANM IACM MASS CGMICGM 9 C 12 12 0.45000 0 10 O 1 16 -0.45000 1 # bonds # NB 10 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 8 27 4 5 27 5 6 6 5 7 6 8 9 27 9 10 5 9 11 10 # bond angles # NBA 14 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 8 13 4 3 8 13 3 4 5 15 4 5 6 22 4 5 7 22 6 5 7 38 3 8 9 15 8 9 10 30 8 9 11 19 10 9 11 33 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 4 1 8 3 2 5 6 7 4 1 9 8 11 10 1 # dihedrals # NDA 6 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 8 39 1 3 4 5 34 1 3 8 9 34 3 4 5 6 40 3 8 9 11 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE SBDH # building block (residue, nucleotide, etc.) # RNME SBDH # stereochemistry at CB atom -> S # improper dihedral angle definition -> CB-CA-N-CG = 35 deg # number of atoms, number of preceding exclusions # NMAT NLIN 11 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 9 2 H 21 1 0.31000 1 1 3 3 CB 14 3 0.00000 0 4 4 5 9 10 4 CG 15 4 0.00000 1 4 5 6 7 9 5 CD 12 12 0.33000 0 3 6 7 8 6 OE1 1 16 -0.45000 0 1 7 7 OE2 3 16 -0.28800 0 1 8 8 HE2 21 1 0.40800 1 0 9 CA 15 4 0.00000 1 3 10 11 12 # trailing atoms #ATOM ANM IACM MASS CGMICGM 10 C 12 12 0.45000 0 11 O 1 16 -0.45000 1 # bonds # NB 11 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 9 27 4 5 27 5 6 5 5 7 13 7 8 1 9 10 27 10 11 5 10 12 10 # bond angles # NBA 15 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 9 13 4 3 9 13 3 4 5 15 4 5 6 30 4 5 7 19 6 5 7 33 5 7 8 12 3 9 10 15 9 10 11 30 9 10 12 19 11 10 12 33 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 4 1 9 3 2 5 6 7 4 1 10 9 12 11 1 # dihedrals # NDA 7 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 9 39 1 3 4 5 34 1 3 9 10 34 3 9 10 12 40 3 4 5 7 40 4 5 7 8 12 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE SBE # building block (residue, nucleotide, etc.) # RNME SBE # stereochemistry at CB atom -> S # improper dihedral angle definition -> CB-N-CA-CG = 35 deg # number of atoms, number of preceding exclusions # NMAT NLIN 11 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 9 2 H 21 1 0.31000 1 1 3 3 CB 14 3 0.00000 0 4 4 5 9 10 4 CG 15 4 0.00000 0 3 5 6 9 5 CD 15 4 0.00000 1 3 6 7 8 6 CE 12 12 0.27000 0 2 7 8 7 OZ1 2 16 -0.63500 0 1 8 8 OZ2 2 16 -0.63500 1 0 9 CA 15 4 0.00000 1 3 10 11 12 # trailing atoms #ATOM ANM IACM MASS CGMICGM 10 C 12 12 0.45000 0 11 O 1 16 -0.45000 1 # bonds # NB 11 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 9 27 4 5 27 5 6 27 6 7 6 6 8 6 9 10 27 10 11 5 10 12 10 # bond angles # NBA 15 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 9 13 4 3 9 15 3 4 5 15 4 5 6 15 5 6 7 22 5 6 8 22 7 6 8 38 3 9 10 15 9 10 11 30 9 10 12 19 11 10 12 33 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 3 1 9 4 2 6 7 8 5 1 10 9 12 11 1 # dihedrals # NDA 7 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 9 39 1 3 4 5 34 1 3 9 10 34 3 4 5 6 34 4 5 6 8 40 3 9 10 12 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE SBEH # building block (residue, nucleotide, etc.) # RNME SBEH # stereochemistry at CB atom -> S # improper dihedral angle definition -> CB-N-CA-CG = 35 deg # number of atoms, number of preceding exclusions # NMAT NLIN 12 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 10 2 H 21 1 0.31000 1 1 3 3 CB 14 3 0.00000 0 4 4 5 10 11 4 CG 15 4 0.00000 0 3 5 6 10 5 CD 15 4 0.00000 1 3 6 7 8 6 CE 12 12 0.33000 0 3 7 8 9 7 OZ1 1 16 -0.45000 0 1 8 8 OZ2 3 16 -0.28800 0 1 9 9 HZ2 21 1 0.40800 1 0 10 CA 15 4 0.00000 1 3 11 12 13 # trailing atoms #ATOM ANM IACM MASS CGMICGM 11 C 12 12 0.45000 0 12 O 1 16 -0.45000 1 # bonds # NB 12 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 10 27 4 5 27 5 6 27 6 7 5 6 8 13 8 9 1 10 11 27 11 12 5 11 13 10 # bond angles # NBA 16 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 10 13 4 3 10 13 3 4 5 15 4 5 6 15 5 6 7 30 5 6 8 19 7 6 8 33 6 8 9 12 3 10 11 15 10 11 12 30 10 11 13 19 12 11 13 33 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 3 1 10 4 2 6 7 8 5 1 11 10 13 12 1 # dihedrals # NDA 8 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 10 39 1 3 4 5 34 3 10 11 13 40 1 3 10 11 34 3 4 5 6 34 4 5 6 8 40 5 6 8 9 12 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE SBQ # building block (residue, nucleotide, etc.) # RNME SBQ # stereochemistry at CB atom -> S # improper dihedral angle definition -> CB-N-CA-CG = 35 deg # number of atoms, number of preceding exclusions # NMAT NLIN 13 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 11 2 H 21 1 0.31000 1 1 3 3 CB 14 3 0.00000 0 4 4 5 11 12 4 CG 15 4 0.00000 0 3 5 6 11 5 CD 15 4 0.00000 1 3 6 7 8 6 CE 12 12 0.29000 0 4 7 8 9 10 7 OZ1 1 16 -0.45000 0 1 8 8 NZ2 7 14 -0.72000 0 2 9 10 9 HZ21 21 1 0.44000 0 1 10 10 HZ22 21 1 0.44000 1 0 11 CA 15 4 0.00000 1 3 12 13 14 # trailing atoms #ATOM ANM IACM MASS CGMICGM 12 C 12 12 0.45000 0 13 O 1 16 -0.45000 1 # bonds # NB 13 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 11 27 4 5 27 5 6 27 6 7 5 6 8 9 8 9 2 8 10 2 11 12 27 12 13 5 12 14 10 # bond angles # NBA 18 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 11 13 4 3 11 13 3 4 5 15 4 5 6 15 5 6 7 30 5 6 8 19 7 6 8 33 6 8 9 23 6 8 10 23 9 8 10 24 3 11 12 15 11 12 13 30 11 12 14 19 13 12 14 33 # improper dihedrals # NIDA 5 # IB JB KB LB MCB 1 -1 3 2 1 3 1 11 4 2 6 7 8 5 1 8 9 10 6 1 12 11 14 13 1 # dihedrals # NDA 8 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 11 39 1 3 4 5 34 1 3 11 12 34 3 4 5 6 34 4 5 6 8 40 5 6 8 9 14 3 11 12 14 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE SBF # building block (residue, nucleotide, etc.) # RNME SBF # stereochemistry at CB atom -> S # improper dihedral angle definition -> CB-N-CA-CG = 35 deg # number of atoms, number of preceding exclusions # NMAT NLIN 18 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 16 2 H 21 1 0.31000 1 1 3 3 CB 14 3 0.00000 0 4 4 5 16 17 4 CG 15 4 0.00000 0 8 5 6 7 8 9 10 12 16 5 CD 12 12 0.00000 1 9 6 7 8 9 10 11 12 13 14 6 CE1 12 12 -0.14000 0 8 7 8 9 10 11 12 14 15 7 HE1 20 1 0.14000 1 4 8 10 11 14 8 CE2 12 12 -0.14000 0 6 9 10 12 13 14 15 9 HE2 20 1 0.14000 1 3 12 13 14 10 CZ1 12 12 -0.14000 0 5 11 12 13 14 15 11 HZ1 20 1 0.14000 1 3 12 14 15 12 CZ2 12 12 -0.14000 0 3 13 14 15 13 HZ2 20 1 0.14000 1 2 14 15 14 CH 12 12 -0.14000 0 1 15 15 HH 20 1 0.14000 1 0 16 CA 15 4 0.00000 1 3 17 18 19 # trailing atoms #ATOM ANM IACM MASS CGMICGM 17 C 12 12 0.45000 0 18 O 1 16 -0.45000 1 # bonds # NB 19 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 16 27 4 5 27 5 6 16 5 8 16 6 7 3 6 10 16 8 9 3 8 12 16 10 11 3 10 14 16 12 13 3 12 14 16 14 15 3 16 17 27 17 18 5 17 19 10 # bond angles # NBA 29 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 16 13 4 3 16 13 3 4 5 15 4 5 6 27 4 5 8 27 6 5 8 27 5 6 7 25 5 6 10 27 7 6 10 25 5 8 9 25 5 8 12 27 9 8 12 25 6 10 11 25 6 10 14 27 11 10 14 25 8 12 13 25 8 12 14 27 13 12 14 25 10 14 12 27 10 14 15 25 12 14 15 25 3 16 17 15 16 17 18 30 16 17 19 19 18 17 19 33 # improper dihedrals # NIDA 15 # IB JB KB LB MCB 1 -1 3 2 1 3 1 16 4 2 5 6 8 4 1 5 6 10 14 1 5 8 12 14 1 6 5 8 12 1 6 5 10 7 1 6 10 14 12 1 8 5 6 10 1 8 5 12 9 1 8 12 14 10 1 11 6 14 10 1 13 8 14 12 1 14 10 12 15 1 17 16 19 18 1 # dihedrals # NDA 6 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 16 39 1 3 4 5 34 1 3 16 17 34 3 4 5 6 40 3 16 17 19 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE BGL # building block (residue, nucleotide, etc.) # RNME BGL # beta glycine # number of atoms, number of preceding exclusions # NMAT NLIN 6 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 3 2 3 4 2 H 21 1 0.31000 1 1 3 3 CB 15 4 0.00000 1 2 4 5 4 CA 15 4 0.00000 1 3 5 6 7 # trailing atoms #ATOM ANM IACM MASS CGMICGM 5 C 12 12 0.45000 0 6 O 1 16 -0.45000 1 # bonds # NB 6 # IB JB MCB 1 2 2 1 3 21 3 4 27 4 5 27 5 6 5 5 7 10 # bond angles # NBA 8 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 3 4 5 15 4 5 6 30 4 5 7 19 6 5 7 33 # improper dihedrals # NIDA 2 # IB JB KB LB MCB 1 -1 3 2 1 5 4 7 6 1 # dihedrals # NDA 4 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 4 39 1 3 4 5 34 3 4 5 7 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE SBHA # building block (residue, nucleotide, etc.) # RNME SBHA # stereochemistry at CB atom -> S # improper dihedral angle definition -> CB-N-CA-CG = 35 deg # number of atoms, number of preceding exclusions # NMAT NLIN 15 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 13 2 H 21 1 0.31000 1 1 3 3 CB 14 3 0.00000 0 4 4 5 13 14 4 CG 15 4 0.00000 1 8 5 6 7 8 9 10 12 13 5 CD 12 12 0.00000 0 7 6 7 8 9 10 11 12 6 NE1 9 14 -0.05000 0 6 7 8 9 10 11 12 7 HE1 21 1 0.31000 0 4 8 10 11 12 8 CE2 12 12 0.00000 0 4 9 10 11 12 9 HE2 20 1 0.14000 0 2 10 12 10 CZ1 12 12 0.00000 0 2 11 12 11 HZ1 20 1 0.14000 0 1 12 12 NZ2 9 14 -0.54000 0 0 13 CA 15 4 0.00000 1 3 14 15 16 # trailing atoms #ATOM ANM IACM MASS CGMICGM 14 C 12 12 0.45000 0 15 O 1 16 -0.45000 1 # bonds 16 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 13 27 4 5 27 5 6 10 5 8 10 6 7 2 6 10 10 8 9 3 8 12 10 10 11 3 10 12 10 13 14 27 14 15 5 14 16 10 # bond angles # NBA 24 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 13 13 4 3 13 13 3 4 5 15 4 5 6 37 4 5 8 37 6 5 8 7 5 6 7 36 5 6 10 7 7 6 10 36 5 8 9 36 5 8 12 7 9 8 12 36 6 10 11 36 6 10 12 7 11 10 12 36 8 12 10 7 3 13 14 15 13 14 15 30 13 14 16 19 15 14 16 33 # improper dihedrals # NIDA 12 # IB JB KB LB MCB 1 -1 3 2 1 3 1 13 4 2 5 6 8 4 1 5 6 10 12 1 5 8 12 10 1 6 5 8 12 1 6 5 10 7 1 6 10 12 8 1 8 5 6 10 1 8 5 12 9 1 10 6 12 11 1 14 13 16 15 1 # dihedrals # NDA 6 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 13 39 1 3 4 5 34 1 3 13 14 34 3 13 14 16 40 3 4 5 6 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE SBHH # building block (residue, nucleotide, etc.) # RNME SBHH # stereochemistry at CB atom -> S # improper dihedral angle definition -> CB-N-CA-CG = 35 deg # number of atoms, number of preceding exclusions # NMAT NLIN 16 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 14 2 H 21 1 0.31000 1 1 3 3 CB 14 3 0.00000 0 4 4 5 14 15 4 CG 15 4 0.00000 1 8 5 6 7 8 9 10 12 14 5 CD 12 12 -0.05000 0 8 6 7 8 9 10 11 12 13 6 NE1 9 14 0.38000 0 7 7 8 9 10 11 12 13 7 HE1 21 1 0.30000 0 4 8 10 11 12 8 CE2 12 12 -0.10000 0 5 9 10 11 12 13 9 HE2 20 1 0.10000 0 3 10 12 13 10 CZ1 12 12 -0.34000 0 3 11 12 13 11 HZ1 20 1 0.10000 0 2 12 13 12 NZ2 9 14 0.31000 0 1 13 13 HZ2 21 1 0.30000 1 0 14 CA 15 4 0.00000 1 3 15 16 17 # trailing atoms #ATOM ANM IACM MASS CGMICGM 15 C 12 12 0.45000 0 16 O 1 16 -0.45000 1 # bonds # NB 17 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 14 27 4 5 27 5 6 10 5 8 10 6 7 2 6 10 10 8 9 3 8 12 10 10 11 3 10 12 10 12 13 2 14 15 27 15 16 5 15 17 10 # bond angles # NBA 26 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 14 13 4 3 14 13 3 4 5 15 4 5 6 37 4 5 8 37 6 5 8 7 5 6 7 36 5 6 10 7 7 6 10 36 5 8 9 36 5 8 12 7 9 8 12 36 6 10 11 36 6 10 12 7 11 10 12 36 8 12 10 7 8 12 13 36 10 12 13 36 3 14 15 15 14 15 16 30 14 15 17 19 16 15 17 33 # improper dihedrals # NIDA 13 # IB JB KB LB MCB 1 -1 3 2 1 3 1 14 4 2 5 6 8 4 1 5 6 10 12 1 5 8 12 10 1 6 5 8 12 1 6 5 10 7 1 6 10 12 8 1 8 5 6 10 1 8 5 12 9 1 10 6 12 11 1 12 8 10 13 1 15 14 17 16 1 # dihedrals # NDA 6 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 14 39 1 3 4 5 34 1 3 14 15 34 3 14 15 17 40 3 4 5 6 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE SBI # building block (residue, nucleotide, etc.) # RNME SBI # stereochemistry at CB atom -> S # improper dihedral angle definition -> CB-CA-N-CG = 35 deg # number of atoms, number of preceding exclusions # NMAT NLIN 10 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 8 2 H 21 1 0.31000 1 1 3 3 CB 14 3 0.00000 1 5 4 5 6 8 9 4 CG 14 3 0.00000 0 4 5 6 7 8 5 CD1 15 4 0.00000 0 2 6 7 6 CD2 16 5 0.00000 0 0 7 CE 16 5 0.00000 1 0 8 CA 15 4 0.00000 1 3 9 10 11 # trailing atoms #ATOM ANM IACM MASS CGMICGM 9 C 12 12 0.45000 0 10 O 1 16 -0.45000 1 # bonds # NB 10 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 8 27 4 5 27 4 6 27 5 7 27 8 9 27 9 10 5 9 11 10 # bond angles # NBA 14 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 8 13 4 3 8 13 3 4 5 15 3 4 6 15 5 4 6 15 4 5 7 15 3 8 9 15 8 9 10 30 8 9 11 19 10 9 11 33 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 4 1 8 3 2 4 5 6 3 2 9 8 11 10 1 # dihedrals # NDA 6 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 8 39 1 3 4 5 34 1 3 8 9 34 3 4 5 7 34 3 8 9 11 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE SBKH # building block (residue, nucleotide, etc.) # RNME SBKH # stereochemistry at CB atom -> S # improper dihedral angle definition -> CB-N-CA-CG = 35 deg # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 12 2 H 21 1 0.31000 1 1 3 3 CB 14 3 0.00000 0 4 4 5 12 13 4 CG 15 4 0.00000 1 3 5 6 12 5 CD 15 4 0.00000 0 2 6 7 6 CE 15 4 0.00000 1 2 7 8 7 CZ 15 4 0.12700 0 4 8 9 10 11 8 NH 8 14 0.12900 0 3 9 10 11 9 HH1 21 1 0.24800 0 2 10 11 10 HH2 21 1 0.24800 0 1 11 11 HH3 21 1 0.24800 1 0 12 CA 15 4 0.00000 1 3 13 14 15 # trailing atoms #ATOM ANM IACM MASS CGMICGM 13 C 12 12 0.45000 0 14 O 1 16 -0.45000 1 # bonds # NB 14 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 12 27 4 5 27 5 6 27 6 7 27 7 8 21 8 9 2 8 10 2 8 11 2 12 13 27 13 14 5 13 15 10 # bond angles # NBA 20 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 12 13 4 3 12 15 3 4 5 15 4 5 6 15 5 6 7 15 6 7 8 15 7 8 9 11 7 8 10 11 7 8 11 11 9 8 10 10 9 8 11 10 10 8 11 10 3 12 13 15 12 13 14 30 12 13 15 19 14 13 15 33 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 3 1 12 4 2 13 12 15 14 1 # dihedrals # NDA 9 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 12 39 1 3 4 5 34 1 3 12 13 34 3 4 5 6 34 4 5 6 7 34 5 6 7 8 34 6 7 8 9 29 3 12 13 15 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE SBL # building block (residue, nucleotide, etc.) # RNME SBL # stereochemistry at CB atom -> S # improper dihedral angle definition -> CB-N-CA-CG = 35 deg # number of atoms, number of preceding exclusions # NMAT NLIN 10 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 8 2 H 21 1 0.31000 1 1 3 3 CB 14 3 0.00000 0 4 4 5 8 9 4 CG 15 4 0.00000 1 4 5 6 7 8 5 CD 14 3 0.00000 0 2 6 7 6 CE1 16 5 0.00000 0 1 7 7 CE2 16 5 0.00000 1 0 8 CA 15 4 0.00000 1 3 9 10 11 # trailing atoms #ATOM ANM IACM MASS CGMICGM 9 C 12 12 0.45000 0 10 O 1 16 -0.45000 1 # bonds # NB 10 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 8 27 4 5 27 5 6 27 5 7 27 8 9 27 9 10 5 9 11 10 # bond angles # NBA 14 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 8 13 4 3 8 15 3 4 5 15 4 5 6 15 4 5 7 15 6 5 7 15 3 8 9 15 8 9 10 30 8 9 11 19 10 9 11 33 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 3 1 8 4 2 4 6 7 5 2 9 8 11 10 1 # dihedrals # NDA 6 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 8 39 1 3 4 5 34 1 3 8 9 34 3 4 5 6 34 3 8 9 11 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE SBM # building block (residue, nucleotide, etc.) # RNME SBM # stereochemistry at CB atom -> S # improper dihedral angle definition -> CB-CA-N-CG = 35 deg # number of atoms, number of preceding exclusions # NMAT NLIN 10 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 8 2 H 21 1 0.31000 1 1 3 3 CB 14 3 0.00000 0 4 4 5 8 9 4 CG 15 4 0.00000 1 3 5 6 8 5 CD 15 4 0.24100 0 2 6 7 6 SE 23 32 -0.48200 0 1 7 7 CZ 16 5 0.24100 1 0 8 CA 15 4 0.00000 1 3 9 10 11 # trailing atoms #ATOM ANM IACM MASS CGMICGM 9 C 12 12 0.45000 0 10 O 1 16 -0.45000 1 # bonds # NB 10 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 8 27 4 5 27 5 6 32 6 7 31 8 9 27 9 10 5 9 11 10 # bond angles # NBA 13 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 8 13 4 3 8 13 3 4 5 15 4 5 6 16 5 6 7 4 3 8 9 15 8 9 10 30 8 9 11 19 10 9 11 33 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 4 1 8 3 2 9 8 11 10 1 # dihedrals # NDA 7 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 8 39 1 3 4 5 34 1 3 8 9 34 3 4 5 6 34 4 5 6 7 26 3 8 9 11 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE SBP # building block (residue, nucleotide, etc.) # RNME SBP # stereochemistry at CB atom -> S # improper dihedral angle definition -> CB-N-CA-CG = 35 deg # number of atoms, number of preceding exclusions # NMAT NLIN 8 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 5 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 0.00000 1 5 2 3 4 5 6 2 CB 14 3 0.00000 0 5 3 4 5 6 7 3 CG 18 4 0.00000 1 3 4 5 6 4 CD 18 4 0.00000 0 1 5 5 CE 18 4 0.00000 1 0 6 CA 15 4 0.00000 1 3 7 8 9 # trailing atoms #ATOM ANM IACM MASS CGMICGM 7 C 12 12 0.45000 0 8 O 1 16 -0.45000 1 # bonds # NB 9 # IB JB MCB 1 2 21 1 5 21 2 3 27 2 6 27 3 4 27 4 5 27 6 7 27 7 8 5 7 9 10 # bond angles # NBA 13 # IB JB KB MCB -1 1 2 31 -1 1 5 31 2 1 5 21 1 2 3 13 1 2 6 13 3 2 6 13 2 3 4 13 3 4 5 13 1 5 4 13 2 6 7 15 6 7 8 30 6 7 9 19 8 7 9 33 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 2 5 1 2 1 6 3 2 7 6 9 8 1 # dihedrals # NDA 8 # IB JB KB LB MCB -2 -1 1 2 14 -1 1 2 6 39 2 1 5 4 39 1 2 3 4 34 1 2 6 7 34 2 3 4 5 34 3 4 5 1 34 2 6 7 9 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE SBR # building block (residue, nucleotide, etc.) # RNME SBR # stereochemistry at CB atom -> S # improper dihedral angle definition -> CB-N-CA-CG = 35 deg # number of atoms, number of preceding exclusions # NMAT NLIN 18 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 16 2 H 21 1 0.31000 1 1 3 3 CB 14 3 0.00000 0 4 4 5 16 17 4 CG 15 4 0.00000 0 3 5 6 16 5 CD 15 4 0.00000 1 2 6 7 6 CE 15 4 0.09000 0 3 7 8 9 7 NZ 11 14 -0.11000 0 4 8 9 10 13 8 HZ 21 1 0.24000 0 1 9 9 CH 12 12 0.34000 0 6 10 11 12 13 14 15 10 NI1 10 14 -0.26000 0 3 11 12 13 11 HI11 21 1 0.24000 0 1 12 12 HI12 21 1 0.24000 0 0 13 NI2 10 14 -0.26000 0 2 14 15 14 HI21 21 1 0.24000 0 1 15 15 HI22 21 1 0.24000 1 0 16 CA 15 4 0.00000 1 3 17 18 19 # trailing atoms #ATOM ANM IACM MASS CGMICGM 17 C 12 12 0.45000 0 18 O 1 16 -0.45000 1 # bonds # NB 18 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 16 27 4 5 27 5 6 27 6 7 21 7 8 2 7 9 11 9 10 11 9 13 11 10 11 2 10 12 2 13 14 2 13 15 2 16 17 27 17 18 5 17 19 10 # bond angles # NBA 25 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 16 13 4 3 16 13 3 4 5 15 4 5 6 15 5 6 7 13 6 7 8 20 6 7 9 33 8 7 9 23 7 9 10 28 7 9 13 28 10 9 13 28 9 10 11 23 9 10 12 23 11 10 12 24 9 13 14 23 9 13 15 23 14 13 15 24 3 16 17 15 16 17 18 30 16 17 19 19 18 17 19 33 # improper dihedrals # NIDA 7 # IB JB KB LB MCB 1 -1 3 2 1 3 1 16 4 2 7 6 9 8 1 9 10 13 7 1 10 11 12 9 1 13 14 15 9 1 17 16 19 18 1 # dihedrals # NDA 11 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 16 39 1 3 4 5 34 1 3 16 17 34 3 4 5 6 34 4 5 6 7 34 5 6 7 9 39 6 7 9 10 14 7 9 10 11 14 7 9 13 14 14 3 16 17 19 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE SBS # building block (residue, nucleotide, etc.) # RNME SBS # stereochemistry at CB atom -> S # improper dihedral angle definition -> CB-CA-N-CG = 35 deg # number of atoms, number of preceding exclusions # NMAT NLIN 9 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 7 2 H 21 1 0.31000 1 1 3 3 CB 14 3 0.00000 1 4 4 5 7 8 4 CG 15 4 0.26600 0 3 5 6 7 5 OD 3 16 -0.67400 0 1 6 6 HD 21 1 0.40800 1 0 7 CA 15 4 0.00000 1 3 8 9 10 # trailing atoms #ATOM ANM IACM MASS CGMICGM 8 C 12 12 0.45000 0 9 O 1 16 -0.45000 1 # bonds # NB 9 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 7 27 4 5 18 5 6 1 7 8 27 8 9 5 8 10 10 # bond angles # NBA 12 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 7 13 4 3 7 13 3 4 5 13 4 5 6 12 3 7 8 15 7 8 9 30 7 8 10 19 9 8 10 33 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 4 1 7 3 2 8 7 10 9 1 # dihedrals # NDA 6 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 7 39 1 3 4 5 34 1 3 7 8 34 3 4 5 6 23 3 7 8 10 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE SBT # building block (residue, nucleotide, etc.) # RNME SBT # stereochemistry at CB atom -> S # improper dihedral angle definition -> CB-CA-N-CG = 35 deg # number of atoms, number of preceding exclusions # NMAT NLIN 10 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 8 2 H 21 1 0.31000 1 1 3 3 CB 14 3 0.00000 1 5 4 5 7 8 9 4 CG 14 3 0.26600 0 4 5 6 7 8 5 OD1 3 16 -0.67400 0 2 6 7 6 HD1 21 1 0.40800 1 0 7 CD2 16 5 0.00000 1 0 8 CA 15 4 0.00000 1 3 9 10 11 # trailing atoms #ATOM ANM IACM MASS CGMICGM 9 C 12 12 0.45000 0 10 O 1 16 -0.45000 1 # bonds # NB 10 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 8 27 4 5 18 4 7 27 5 6 1 8 9 27 9 10 5 9 11 10 # bond angles # NBA 14 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 8 13 4 3 8 13 3 4 5 13 3 4 7 15 5 4 7 15 4 5 6 12 3 8 9 15 8 9 10 30 8 9 11 19 10 9 11 33 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 4 1 8 3 2 4 5 7 3 2 9 8 11 10 1 # dihedrals # NDA 6 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 8 39 1 3 4 5 34 1 3 8 9 34 3 4 5 6 23 3 8 9 11 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE SBV # building block (residue, nucleotide, etc.) # RNME SBV # stereochemistry at CB atom -> S # improper dihedral angle definition -> CB-CA-N-CG = 35 deg # number of atoms, number of preceding exclusions # NMAT NLIN 9 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 7 2 H 21 1 0.31000 1 1 3 3 CB 14 3 0.00000 0 5 4 5 6 7 8 4 CG 14 3 0.00000 0 3 5 6 7 5 CD1 16 5 0.00000 0 1 6 6 CD2 16 5 0.00000 1 0 7 CA 15 4 0.00000 1 3 8 9 10 # trailing atoms #ATOM ANM IACM MASS CGMICGM 8 C 12 12 0.45000 0 9 O 1 16 -0.45000 1 # bonds # NB 9 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 7 27 4 5 27 4 6 27 7 8 27 8 9 5 8 10 10 # bond angles # NBA 13 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 7 13 4 3 7 15 3 4 5 15 3 4 6 15 5 4 6 15 3 7 8 15 7 8 9 30 7 8 10 19 9 8 10 33 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 4 1 7 3 2 3 5 6 4 2 8 7 10 9 1 # dihedrals # NDA 5 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 7 39 1 3 4 5 34 1 3 7 8 34 3 7 8 10 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE SBY # building block (residue, nucleotide, etc.) # RNME SBY # stereochemistry at CB atom -> S # improper dihedral angle definition -> CB-N-CA-CG = 35 deg # number of atoms, number of preceding exclusions # NMAT NLIN 19 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 17 2 H 21 1 0.31000 1 1 3 3 CB 14 3 0.00000 0 4 4 5 17 18 4 CG 15 4 0.00000 0 8 5 6 7 8 9 10 12 17 5 CD 12 12 0.00000 1 9 6 7 8 9 10 11 12 13 14 6 CE1 12 12 -0.14000 0 8 7 8 9 10 11 12 14 15 7 HE1 20 1 0.14000 1 4 8 10 11 14 8 CE2 12 12 -0.14000 0 6 9 10 12 13 14 15 9 HE2 20 1 0.14000 1 3 12 13 14 10 CZ1 12 12 -0.14000 0 5 11 12 13 14 15 11 HZ1 20 1 0.14000 1 3 12 14 15 12 CZ2 12 12 -0.14000 0 3 13 14 15 13 HZ2 20 1 0.14000 1 2 14 15 14 CH 12 12 0.20300 0 2 15 16 15 OI 3 16 -0.61100 0 1 16 16 HI 21 1 0.40800 1 0 17 CA 15 4 0.00000 1 3 18 19 20 # trailing atoms #ATOM ANM IACM MASS CGMICGM 18 C 12 12 0.45000 0 19 O 1 16 -0.45000 1 # bonds # NB 20 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 17 27 4 5 27 5 6 16 5 8 16 6 7 3 6 10 16 8 9 3 8 12 16 10 11 3 10 14 16 12 13 3 12 14 16 14 15 13 15 16 1 17 18 27 18 19 5 18 20 10 # bond angles # NBA 30 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 17 13 4 3 17 13 3 4 5 15 4 5 6 27 4 5 8 27 6 5 8 27 5 6 7 25 5 6 10 27 7 6 10 25 5 8 9 25 5 8 12 27 9 8 12 25 6 10 11 25 6 10 14 27 11 10 14 25 8 12 13 25 8 12 14 27 13 12 14 25 10 14 12 27 10 14 15 27 12 14 15 27 14 15 16 12 3 17 18 15 17 18 19 30 17 18 20 19 19 18 20 33 # improper dihedrals # NIDA 15 # IB JB KB LB MCB 1 -1 3 2 1 3 1 17 4 2 5 6 8 4 1 5 6 10 14 1 5 8 12 14 1 6 5 8 12 1 6 5 10 7 1 6 10 14 12 1 8 5 6 10 1 8 5 12 9 1 8 12 14 10 1 11 6 14 10 1 13 8 14 12 1 14 10 12 15 1 18 17 20 19 1 # dihedrals # NDA 7 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 17 39 1 3 4 5 34 1 3 17 18 34 3 4 5 6 40 10 14 15 16 11 3 17 18 20 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE SBW # building block (residue, nucleotide, etc.) # RNME SBW # stereochemistry at CB atom -> S # improper dihedral angle definition -> CB-N-CA-CG = 35 deg # number of atoms, number of preceding exclusions # NMAT NLIN 22 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 20 2 H 21 1 0.31000 1 1 3 3 CB 14 3 0.00000 0 4 4 5 20 21 4 CG 15 4 0.00000 1 8 5 6 7 8 9 11 12 20 5 CD 12 12 -0.21000 0 10 6 7 8 9 10 11 12 13 14 16 6 CE1 12 12 -0.14000 0 7 7 8 9 10 11 12 14 7 HE1 20 1 0.14000 0 4 8 9 10 11 8 CE2 12 12 0.00000 0 10 9 10 11 12 13 14 15 16 17 18 9 NZ1 9 14 -0.10000 0 6 10 11 12 14 15 18 10 HZ1 21 1 0.31000 0 2 11 14 11 CZ2 12 12 0.00000 1 7 12 13 14 15 16 18 19 12 CZ3 12 12 -0.14000 0 6 13 14 16 17 18 19 13 HZ3 20 1 0.14000 1 3 16 17 18 14 CH2 12 12 -0.14000 0 5 15 16 17 18 19 15 HH2 20 1 0.14000 1 3 16 18 19 16 CH3 12 12 -0.14000 0 3 17 18 19 17 HH3 20 1 0.14000 1 2 18 19 18 CI2 12 12 -0.14000 0 1 19 19 HI2 20 1 0.14000 1 0 20 CA 15 4 0.00000 1 3 21 22 23 # trailing atoms #ATOM ANM IACM MASS CGMICGM 21 C 12 12 0.45000 0 22 O 1 16 -0.45000 1 # bonds # NB 24 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 20 27 4 5 27 5 6 10 5 8 16 6 7 3 6 9 10 8 11 16 8 12 16 9 10 2 9 11 10 11 14 16 12 13 3 12 16 16 14 15 3 14 18 16 16 17 3 16 18 16 18 19 3 20 21 27 21 22 5 21 23 10 # bond angles # NBA 38 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 20 13 4 3 20 13 3 4 5 15 4 5 6 37 4 5 8 37 6 5 8 7 5 6 7 36 5 6 9 7 7 6 9 36 5 8 11 7 5 8 12 39 11 8 12 27 6 9 10 36 6 9 11 7 10 9 11 36 8 11 9 7 8 11 14 27 9 11 14 39 8 12 13 25 8 12 16 27 13 12 16 25 11 14 15 25 11 14 18 27 15 14 18 25 12 16 17 25 12 16 18 27 17 16 18 25 14 18 16 27 14 18 19 25 16 18 19 25 3 20 21 15 20 21 22 30 20 21 23 19 22 21 23 33 # improper dihedrals # NIDA 23 # IB JB KB LB MCB 1 -1 3 2 1 3 1 20 4 2 5 6 8 4 1 5 6 9 11 1 5 8 11 9 1 6 5 8 11 1 6 5 9 7 1 6 9 11 8 1 8 5 6 9 1 8 11 12 5 1 8 11 14 18 1 8 12 16 18 1 9 6 11 10 1 11 8 12 16 1 11 8 14 9 1 11 14 18 16 1 12 8 11 14 1 12 8 16 13 1 12 16 18 14 1 14 11 18 15 1 16 12 18 17 1 18 14 16 19 1 21 20 23 22 1 # dihedrals # NDA 6 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 20 39 1 3 4 5 34 1 3 20 21 34 3 4 5 8 40 3 20 21 22 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE SRAM # building block (residue, nucleotide, etc.) # RNME SRAM # stereochemistry at CB atom -> S # improper dihedral angle definition -> CB-N-CA-CG = 35 deg # stereochemistry at CA atom -> R # improper dihedral angle definition -> CA-CB-C-CG = 35 deg # number of atoms, number of preceding exclusions # NMAT NLIN 8 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 5 2 H 21 1 0.31000 1 1 3 3 CB 14 3 0.00000 0 4 4 5 6 7 4 CG 16 5 0.00000 1 1 5 5 CA 14 3 0.00000 0 4 6 7 8 9 6 CD 16 5 0.00000 1 1 7 # trailing atoms #ATOM ANM IACM MASS CGMICGM 7 C 12 12 0.45000 0 8 O 1 16 -0.45000 1 # bonds # NB 8 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 5 27 5 6 27 5 7 27 7 8 5 7 9 10 # bond angles # NBA 12 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 5 13 4 3 5 15 3 5 6 15 3 5 7 13 6 5 7 15 5 7 8 30 5 7 9 19 8 7 9 33 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 3 1 5 4 2 5 3 7 6 2 7 5 9 8 1 # dihedrals # NDA 4 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 5 39 1 3 5 7 34 3 5 7 9 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE SRLM # building block (residue, nucleotide, etc.) # RNME SRLM # stereochemistry at CB atom -> S # improper dihedral angle definition -> CB-N-CA-CG = 35 deg # stereochemistry at CA atom -> R # improper dihedral angle definition -> CA-CB-C-CG = 35 deg # number of atoms, number of preceding exclusions # NMAT NLIN 11 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 8 2 H 21 1 0.31000 1 1 3 3 CB 14 3 0.00000 0 5 4 5 8 9 10 4 CG 15 4 0.00000 1 4 5 6 7 8 5 CD 14 3 0.00000 0 2 6 7 6 CE1 16 5 0.00000 0 1 7 7 CE2 16 5 0.00000 1 0 8 CA 14 3 0.00000 0 4 9 10 11 12 9 CZ 16 5 0.00000 1 1 10 # trailing atoms #ATOM ANM IACM MASS CGMICGM 10 C 12 12 0.45000 0 11 O 1 16 -0.45000 1 # bonds # NB 11 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 8 27 4 5 27 5 6 27 5 7 27 8 9 27 8 10 27 10 11 5 10 12 10 # bond angles # NBA 16 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 8 13 4 3 8 15 3 4 5 15 4 5 6 15 4 5 7 15 6 5 7 15 3 8 9 15 3 8 10 13 9 8 10 15 8 10 11 30 8 10 12 19 11 10 12 33 # improper dihedrals # NIDA 5 # IB JB KB LB MCB 1 -1 3 2 1 3 1 8 4 2 4 6 7 5 2 8 3 10 9 2 10 8 12 11 1 # dihedrals # NDA 6 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 8 39 1 3 4 5 34 1 3 8 10 34 3 4 5 6 34 3 8 10 12 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE SRVM # building block (residue, nucleotide, etc.) # RNME SRVM # stereochemistry at CB atom -> S # improper dihedral angle definition -> CB-N-CA-CG = 35 deg # stereochemistry at CA atom -> R # improper dihedral angle definition -> CA-CB-C-CG = 35 deg # number of atoms, number of preceding exclusions # NMAT NLIN 10 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 7 2 H 21 1 0.31000 1 1 3 3 CB 14 3 0.00000 0 6 4 5 6 7 8 9 4 CG 14 3 0.00000 0 3 5 6 7 5 CD1 16 5 0.00000 0 1 6 6 CD2 16 5 0.00000 1 0 7 CA 14 3 0.00000 0 4 8 9 10 11 8 CE 16 5 0.00000 1 1 9 # trailing atoms #ATOM ANM IACM MASS CGMICGM 9 C 12 12 0.45000 0 10 O 1 16 -0.45000 1 # bonds # NB 10 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 7 27 4 5 27 4 6 27 7 8 27 7 9 27 9 10 5 9 11 10 # bond angles # NBA 15 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 7 13 4 3 7 15 3 4 5 15 3 4 6 15 5 4 6 15 3 7 8 15 3 7 9 13 8 7 9 15 7 9 10 30 7 9 11 19 10 9 11 33 # improper dihedrals # NIDA 5 # IB JB KB LB MCB 1 -1 3 2 1 3 1 7 4 2 3 5 6 4 2 7 3 9 8 2 9 7 11 10 1 # dihedrals # NDA 5 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 7 39 1 3 4 5 34 1 3 7 9 34 3 7 9 11 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6_beta.dat SOL TYPE SSAM # building block (residue, nucleotide, etc.) # RNME SSAM # stereochemistry at CB atom -> S # stereochemistry at CA atom -> S # improper dihedral angle definition -> CB-N-CA-CG = 35 deg # improper dihedral angle definition -> CA-C-CB-CD = 35 deg # number of atoms, number of preceding exclusions # NMAT NLIN 8 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 5 2 H 21 1 0.31000 1 1 3 3 CB 14 3 0.00000 0 4 4 5 6 7 4 CG 16 5 0.00000 1 1 5 5 CA 14 3 0.00000 0 4 6 7 8 9 6 CD 16 5 0.00000 1 1 7 # trailing atoms #ATOM ANM IACM MASS CGMICGM 7 C 12 12 0.45000 0 8 O 1 16 -0.45000 1 # bonds # NB 8 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 5 27 5 6 27 5 7 27 7 8 5 7 9 10 # bond angles # NBA 12 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 5 13 4 3 5 15 3 5 6 15 3 5 7 13 6 5 7 15 5 7 8 30 5 7 9 19 8 7 9 33 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 3 1 5 4 2 6 3 7 5 2 7 5 9 8 1 # dihedrals # NDA 4 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 5 39 1 3 5 7 34 3 5 7 9 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLEND #@BLOCKTYPE mtb53a6_beta.dat INI TYPE BH3+ # building block (residue, nucleotide, etc.) # RNME BH3+ # number of atoms, number of atoms to be replaced # NMAT NREP 5 3 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 H1 21 1 0.24800 0 4 2 3 4 5 2 H2 21 1 0.24800 0 3 3 4 5 # replacing atoms 3 N 8 14 0.12900 0 4 H3 21 1 0.24800 0 5 CB 14 3 0.12700 1 # bonds # NB 2 # IB JB MCB 1 3 2 2 3 2 # bond angles # NBA 6 # IB JB KB MCB 1 3 2 10 1 3 4 10 1 3 5 11 2 3 4 10 2 3 5 11 4 3 5 11 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 1 # IB JB KB LB MCB 2 3 5 6 29 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLEND #@BLOCKTYPE mtb53a6_beta.dat INI TYPE BH2 # building block (residue, nucleotide, etc.) # RNME BH2 # number of atoms, number of atoms to be replaced # NMAT NREP 4 3 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 H1 21 1 0.44000 0 3 2 3 4 # replacing atoms 2 N 7 14 -0.64000 0 3 H2 21 1 0.44000 0 4 CB 14 3 -0.24000 1 # bonds # NB 1 # IB JB MCB 1 2 2 # bond angles # NBA 3 # IB JB KB MCB 1 2 3 10 1 2 4 11 3 2 4 11 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 1 # IB JB KB LB MCB 1 2 4 5 29 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLEND #@BLOCKTYPE mtb53a6_beta.dat TER TYPE BOO- # building block (residue, nucleotide, etc.) # RNME BOO- # number of atoms, number of atoms to be replaced # NMAT NREP 3 -2 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C 12 12 0.27000 0 2 2 3 2 O1 2 16 -0.63500 0 1 3 3 O2 2 16 -0.63500 1 0 # bonds # NB 2 # IB JB MCB 1 2 6 1 3 6 # bond angles # NBA 3 # IB JB KB MCB 0 1 2 22 0 1 3 22 2 1 3 38 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLEND #@BLOCKTYPE mtb53a6_beta.dat TER TYPE BOOH # building block (residue, nucleotide, etc.) # RNME BOOH # number of atoms, number of atoms to be replaced # NMAT NREP 4 -2 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C 12 12 0.33000 0 3 2 3 4 2 O1 1 16 -0.45000 0 1 3 3 O2 3 16 -0.28800 0 1 4 4 H 21 1 0.40800 1 0 # bonds # NB 3 # IB JB MCB 1 2 5 1 3 13 3 4 1 # bond angles # NBA 1 # IB JB KB MCB 1 3 4 12 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 1 # IB JB KB LB MCB 0 1 3 4 12 #@FREELINE # LJ exceptions # NEX 0 END